We described the vegetation of two alluvial swamp forest stands along Durham Creek in Beaufort County, North Carolina, USA in relation to elevation, hydrologic, and edaphic gradients. Over 3,000 surveyed elevations of individual plant microsites were used in conjunction with 26 years of stream gage data to examine individual species responses to annual and growing season flooding frequencies. Direct gradient analyses combined with plot ordinations derived from detrended correspondence analysis and canonical correspondence analysis suggested that differences in vegetation between the stands were primarily the result of variations in elevation, growing season flooding frequency, percent base saturation, exchangeable acidity, and soil physical properties. Although the stands were less than 4.5 km apart and without significant intermediate tributaries, growing season flooding frequency and duration were magnified in the lowest elevations of the downstream stand. An elevation difference of as little as 10 cm resulted in a 20% difference in the frequency of surface flooding during the growing season. Species distributions were significantly correlated with depth to mottling (r² = 0.75), flooding frequency (r² = −0.57), elevation (r² = 0.70), and several soil chemical properties. The two stands had very similar annual surface flooding regimes, but subtle differences in growing season flooding frequency, soil characteristics, and disturbance history have apparently resulted in dissimilar plant community composition and structure. These results suggest that the lack of quantitative data on vegetation-environment interactions occurring at the microtopographic scale (10⁻¹ m) in alluvial swamp forests makes precise prediction, planning, or design of created or restored wetland composition and function a formidable challenge.